INSTRUCTOR
Nevin Dale Young
320 Cargill Genomics Building
612-625-2225
Email: neviny@umn.edu
Home page:
http://umn.edu/home/neviny
TEACHING ASSISTANT
Roman Briskine
305 Cargill Genomics Building
612-626-2692
Email: brisk022@umn.edu
Office hours are flexible. Students
are encouraged to email either of us to make an appointment or to visit
informally before or after class.
SYLLABUS
Overview
Plant genomics is a course for graduate and advanced undergraduate students who are interested in the application of genomics and bioinformatics to the study of plants. Students learn strategies for structural and functional genomic analysis by exploring the genomes of model plant systems, comparative genomics, genome expression and genome evolution. Students also learn the fundamentals of sequence analysis, database searching and data-mining through computer labs and independent projects. Class sessions consist of lectures, discussions, small group activities and hands-on computer labs.
Prerequisites
Introductory courses in genetics and either biochemistry or cell biology – or – consent of instructor.
In Plant Genomics
students learn:
Requirements
Everyone who attends class must enroll formally. This includes students who are taking Plant Genomics for credit, as well as students who plan to audit. Because class participation is a formal part of the final grade, students should plan to attend every class. If you do need to miss a class for a valid reason, please inform the instructor by email a day or two ahead of time. Active participation is expected every day, so assigned readings should be completed before coming to class.
Readings
Nearly all readings are found through the internet, with links listed below.
Exams
There will be two exams, one on October 21st and another on December 14th. There will not be make-ups, so please plan on being in class these days. Each exam will consist of five to ten "medium" answer questions.
Computer Homeworks
To provide practical experience with genome databases and the process of "data-mining", there will be a variety of primarily computer-related homework assignments. These homeworks will be relatively short and usually associated with one of the labs. The final computer homework will be a multi-week assignment (starting approximately October 26th) consisting of an internet-based project and student presentations. On the final project, students will be working in small groups. Students will be expected to turn in both group and individual reports electronically for this multi-week assignment.
Class Participation
There will be regular "break-out" sessions and other class-wide discussions throughout the semester. Students are expected to participate actively. Responsibilities will be distributed among everyone in the group. Class participation will be noted and included in the final grade, especially in cases of "borderline" grades.
Grade Disputes
All grade disputes should be submitted in writing (or email) to the instructor within one week of receiving the disputed grade. If the dispute can not be resolved satisfactorily, the assignment will be given to an expert outside of class to provide input. Please remember that re-graded exams and assignments can be lowered as well as raised.
Students with Disabilities
Students with any type of disability will be accommodated. For assistance, please contact University Disability Services (612-624-4037) or the instructor.
Scholastic Honesty Policy
Students in Plant
Genomics are expected to do their own work and submit their own
assignments (unless explicitly stated otherwise). Nonetheless, group
activities and discussion among students are strongly encouraged. Except
when
explicitly
announced by the instructor or in homework
instructions, students are prohibited from copying and pasting
materials directly from the internet.
Details on the University of Minnesota's student honor code is found
at: http://www1.umn.edu/regents/policies/academic/StudentConduct.pdf.
September 7, 2010: Global
Views of
Biology
September 14, 2010: DNA Sequencing, Arrays
and Mutants
Wikipedia: Polymerase Chain Reaction
PCR technologyWikipedia: DNA sequencing
Cycle DNA sequencing
Illumina sequencing technology
Wikipedia: DNA microarrays
DNA microarrays
Genechips
Wikipedia: Genetic Screens & Reverse Genetics
September 16, 2010: Aligning and Searching DNA Sequences 1
Wikipedia: BLAST
Pevsner
J
(2009)
Bioinformatics
and
Functional
Genomics,
Vol.
2.
Wiley-Blackwell.
Pages
47-76.
September 21, 2010: Aligning and Searching DNA Sequences 2
Wikipedia:
Multiple
sequence
alignment
Pevsner
J
(2009)
Bioinformatics
and
Functional
Genomics,
Vol.
2.
Wiley-Blackwell.
Pages
179-190 & 197-203.
September 23, 2010: Searching Genome Databases
(LAB)
September 28, 2010: EST Libraries, Transcript Assemblies &
Gene Indices
Wikipedia: Expressed sequence tags
Nagaraj SH et al (2007) A hitchhiker's
guide to expressed sequence tag (EST) analysis. Briefings in
Bioinformatics 8:6-21.
September 30, 2010: Exploring Gene Indices (LAB)
Quakenbush
J
et
al
(2001)
The
TIGR
gene
indices:
Analysis
of
gene
transcript
sequences
in
highly
sampled
eukaryotic species. Nucleic
Acids Research 29: 159-164.
October 5, 2010: Sequencing Plant Genomes
October 7, 2010: The
Arabidopsis
Genome
Dolan Center: "Chromosome 11 Flyover"
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
October 12, 2010: Genome Duplication and Synteny
October 28, 2010: Microarrays, DNA Chips and RNA-SeqWortman JR, et al (2003) Annotating the Arabidopsis genome. Plant Physiology 132: 461-468.
September
7,
2010:
Global
Views of
Biology
September 14, 2010: DNA Sequencing, Arrays and Mutants
September
16,
2010:
Aligning and Searching DNA Sequences 1
September
21,
2010:
Aligning
and
Searching
DNA
Sequences
2
September
21,
2010:
Perl
Module
September
23,
2010:
Searching
Genome
Databases
(LAB) See also computer lab handouts below
September
28,
2010:
EST
Libraries
September
30,
2010:
Exploring
Gene
Indices (LAB) See also computer lab handouts below
October
5,
2010:
Sequencing
Plant Genomes
October
7,
2010: The Arabidopsis
Genome
October
12,
2010:
Comparative Genomics
September 23, 2010: Genome Databases & Blast
Final Exam -- 2009
September 8, 2009: Global
Views of
Biology
Lander ES (1996) The new genomics: Global views of biology. Science 274: 536.
September 10, 2009: DNA Sequencing and DNA
Chips
PCR technology
Sanger DNA sequencing
Cycle DNA sequencing
Solexa sequencing technology
DNA microarrays
Genechips
September 15, 2009: Aligning DNA Sequences
Pevsner J (2009)
Bioinformatics and Functional Genomics, Vol. 2. Wiley-Blackwell. Pages
47-76.
September 17, 2009: Searching Genome Databases
(LAB)
September 22, 2009: EST Libraries
September 24, 2009: Exploring Gene Indices (LAB)
Quakenbush
J
et
al
(2001)
The
TIGR
gene
indices:
Analysis
of
gene
transcript
sequences
in
highly
sampled
eukaryotic species. Nucleic
Acids Research 29: 159-164.
September 29, 2009: Sequencing Plant Genomes
Pevsner J (2009)
Bioinformatics and Functional Genomics,
Vol. 2. Wiley-Blackwell. Pages 537-554.
October 1, 2009: Arabidopsis
Genome
Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
October 6, 2009: Comparative Genomics
October 20, 2009: Microarrays & DNA ChipsWortman JR, et al (2003) Annotating the Arabidopsis genome. Plant Physiology 132: 461-468.
Global
Views
of
Biology
(September
8,
2009)
Homework
#1:
Sequence
Alignment
and
Genome
Databases
(September
17,
2009)
Homework
#2:
Exploring
&
Annotating
Plant
Genomes
(Due
October
15,
2009)
Homework
#3:
Microarray
Analysis
of
Gene
Expression
(Due
November
10,
2009)
Homework
#4:
Data
Mining
Group
Project
(Due
December
7,
2009)
Last update: November 26, 2010
©
1998-2010 by Nevin Dale Young and the Regents of the University of
Minnesota
The University of Minnesota is an equal opportunity educator and
employer.